ok here's my 2 cents...
1. have weather
2. let us play with it. (swirl the clouds.)
3. let us play with the the environment (here's an Idea, changing the course of streams or carving into mountains or moving the ocean back and forth. Dude this is a freaking GOD game. let us ***** around with stuff...)
4. miracle that affect the environment ( making rain outa the water miracle or burning trees to make feralizer.)
5. smarter AI is a obvious thing & creature pathfinding
6. Animal size is fine to me but make skins lionhead! ( WE LOVE VARIATION! )
7. make it possible for modders to make new Animals without taking the place of others
8. make the military units deeper.
9. consciences that talk! and People that says stuff like " our God is so strong!"
10. MOST IMPORTANTLY! Immerse your Players into the world!